SMTL ID : 4jx6.1 (2 other biounits)

Structure of the carboxyl transferase domain Y628A from Rhizobium etli pyruvate carboxylase with pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-tetramer

Ligands

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 8 residues within 4Å: Chain A: R.113, Q.117, G.151, L.184, R.186, K.283, V.446, T.447 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.446 Hydrogen bonds: A:R.113, A:Q.117 Water bridges: A:R.113 Salt bridges: A:R.186 PYR.4: 9 residues within 4Å: Chain B: R.113, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, T.447 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.113, B:R.113, B:Q.117, B:T.447 Salt bridges: B:R.186

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.114, K.283, H.312, H.314 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, A:H.312, A:H.314, H2O.1 ZN.5: 5 residues within 4Å: Chain B: D.114, K.283, H.312, H.314, Q.348 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.114, B:H.312, B:H.314, H2O.2 ZN.8: 4 residues within 4Å: Chain C: D.114, K.283, H.312, H.314 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.114, C:H.312, C:H.314, H2O.2 ZN.10: 5 residues within 4Å: Chain D: D.114, K.283, H.312, H.314, Q.348 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.114, D:H.312, D:H.314

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: M.99, R.100, E.102, D.333 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:M.99, A:R.100, A:E.102, A:D.333 MG.6: 5 residues within 4Å: Chain B: M.99, R.100, N.101, E.102, D.333 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.99, B:R.100, B:D.333, H2O.2, H2O.2 MG.9: 4 residues within 4Å: Chain C: M.99, R.100, E.102, D.333 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.99, C:R.100, C:E.102, C:D.333, H2O.2 MG.11: 5 residues within 4Å: Chain D: M.99, R.100, N.101, E.102, D.333 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:M.99, D:E.102, D:D.333, H2O.3, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: D.315, G.318, G.344, N.345 Chain C: D.315, G.318, G.344, N.345 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:D.315, C:N.345, A:D.315, A:N.345, A:N.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lietzan, A.D. et al., A Substrate-induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase. J.Biol.Chem. (2013)

Release Date

2013-05-29

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase

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